Gmx Check — GROMACS 2022.2 Documentation

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Back to top View this page Edit this page Toggle Light / Dark / Auto color theme Toggle table of contents sidebar gmx check¶

Synopsis¶

gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]] [-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]] [-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>] [-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>] [-abstol <real>] [-[no]ab] [-lastener <string>]

Description¶

gmx check reads a trajectory (.tng, .trr or .xtc), an energy file (.edr) or an index file (.ndx) and prints out useful information about them.

Option -c checks for presence of coordinates, velocities and box in the file, for close contacts (smaller than -vdwfac and not bonded, i.e. not between -bonlo and -bonhi, all relative to the sum of both Van der Waals radii) and atoms outside the box (these may occur often and are no problem). If velocities are present, an estimated temperature will be calculated from them.

If an index file, is given its contents will be summarized.

If both a trajectory and a .tpr file are given (with -s1) the program will check whether the bond lengths defined in the tpr file are indeed correct in the trajectory. If not you may have non-matching files due to e.g. deshuffling or due to problems with virtual sites. With these flags, gmx check provides a quick check for such problems.

The program can compare two run input (.tpr) files when both -s1 and -s2 are supplied. When comparing run input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance set to zero to find any differences not due to minor compiler optimization differences, although you can of course still set any other tolerances through the options. Similarly a pair of trajectory files can be compared (using the -f2 option), or a pair of energy files (using the -e2 option).

For free energy simulations the A and B state topology from one run input file can be compared with options -s1 and -ab.

Options¶

Options to specify input files:

-f [<.xtc/.trr/…>] (traj.xtc) (Optional)

Trajectory: xtc trr cpt gro g96 pdb tng h5md

-f2 [<.xtc/.trr/…>] (traj.xtc) (Optional)

Trajectory: xtc trr cpt gro g96 pdb tng h5md

-s1 [<.tpr>] (top1.tpr) (Optional)

Portable xdr run input file

-s2 [<.tpr>] (top2.tpr) (Optional)

Portable xdr run input file

-c [<.tpr/.gro/…>] (topol.tpr) (Optional)

Structure+mass(db): tpr gro g96 pdb brk ent

-e [<.edr>] (ener.edr) (Optional)

Energy file

-e2 [<.edr>] (ener2.edr) (Optional)

Energy file

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-m [<.tex>] (doc.tex) (Optional)

LaTeX file

Other options:

-vdwfac <real> (0.8)

Fraction of sum of VdW radii used as warning cutoff

-bonlo <real> (0.4)

Min. fract. of sum of VdW radii for bonded atoms

-bonhi <real> (0.7)

Max. fract. of sum of VdW radii for bonded atoms

-[no]rmsd (no)

Print RMSD for x, v and f

-tol <real> (0.001)

Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)

-abstol <real> (0.001)

Absolute tolerance, useful when sums are close to zero.

-[no]ab (no)

Compare the A and B topology from one file

-lastener <string>

Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.

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